Bit perfect CD copying (ala EAC)
Unsure
Peer 2 peer file sharing programs (i.e. bit torrent, direct connect, limewire and usenet)
Lime wire, Bit Torrent, Azeraus, usenet all available for mac since time began.
Compressed file encoding (other than mp3 or apple, example musepack, ogg vorbis, flac, monkeys audio, div X, X vid etc etc)
Flak, etc is all available as free downloads, its not built into the OS any more than it is on PC.
Disc cloning software (like Clone CD)
There is a lot, none the least of which is Disk Utility which is part of the OS, it also creates .DMG files, I am not sure if these exist on PCs, but in essence mounts like a seperate drive, handy for putting CDs onto your harddrive.
Java based VNC server / client (like Real and Ultra VNC) - for controlling home PC through web browser at a remote site?
Chicken of VNC is free and works flawlessly for me, others are available.
Chat clients - MSN Messenger, MIRC etc etc
iChat comes as part of the OS and has no peer for video chat. MSN, AOL, Andium etc all available for mac as PC.
Freeware photo editing - i.e. GIMP
Gimp works on Mac once you have installed X11, they are apparently working on a native one.
Freeware antivirus - i.e. AVG Free
ClamXV
Compatability with USB devices - not just IPOD, but rival players, digital cameras, etc.
I have thrown many a digital camera at it with no issues. iRivers and any other harddrive or flash based device should load as a harddrive no problems, as do Card readers etc etc.
One of the quickest ways to see whats out there is a scan round apple.com click on OSX then software, or have a look at
www.macupdate.com